This paper describes a probabilistic framework for studying associations between multiple genotypes, biomarkers, and phenotypic traits in the presence of noise and unobserved confounders for large genetic studies. The framework builds on sparse linear methods developed for regression and modified here for inferring causal structures of richer networks with latent variables. The method is motivated by the use of genotypes as ``instruments'' to infer causal associations between phenotypic biomarkers and outcomes, without making the common restrictive assumptions of instrumental variable methods. The method may be used for an effective screening of potentially interesting genotype phenotype and biomarker-phenotype associations in genome-wide studies, which may have important implications for validating biomarkers as possible proxy endpoints for early stage clinical trials. Where the biomarkers are gene transcripts, the method can be used for fine mapping of quantitative trait loci (QTLs) detected in genetic linkage studies. The method is applied for examining effects of gene transcript levels in the liver on plasma HDL cholesterol levels for a sample of sequenced mice from a heterogeneous stock, with $\sim 10^5$ genetic instruments and $\sim 47 \times 10^3$ gene transcripts.

This paper presents Bayesian non-parametric models that simultaneously learn to segment words from phoneme strings and learn the referents of some of those words, and shows that there is a synergistic interaction in the acquisition of these two kinds of linguistic information. The models themselves are novel kinds of Adaptor Grammars that are an extension of an embedding of topic models into PCFGs. These models simultaneously segment phoneme sequences into words and learn the relationship between non-linguistic objects to the words that refer to them. We show (i) that modelling inter-word dependencies not only improves the accuracy of the word segmentation but also of word-object relationships, and (ii) that a model that simultaneously learns word-object relationships and word segmentation segments more accurately than one that just learns word segmentation on its own. We argue that these results support an interactive view of language acquisition that can take advantage of synergies such as these.

Heavy-tailed distributions naturally occur in many real life problems. Unfortunately, it is typically not possible to compute inference in closed-form in graphical models which involve such heavy tailed distributions. In this work, we propose a novel simple linear graphical model for independent latent random variables, called linear characteristic model (LCM), defined in the characteristic function domain. Using stable distributions, a heavy-tailed family of distributions which is a generalization of Cauchy, L\'evy and Gaussian distributions, we show for the first time, how to compute both exact and approximate inference in such a linear multivariate graphical model. LCMs are not limited to only stable distributions, in fact LCMs are always defined for any random variables (discrete, continuous or a mixture of both). We provide a realistic problem from the field of computer networks to demonstrate the applicability of our construction. Other potential application is iterative decoding of linear channels with non-Gaussian noise.

We develop an online variational Bayes (VB) algorithm for Latent Dirichlet Allocation (LDA). Online LDA is based on online stochastic optimization with a natural gradient step, which we show converges to a local optimum of the VB objective function. It can handily analyze massive document collections, including those arriving in a stream. We study the performance of online LDA in several ways, including by fitting a 100-topic topic model to 3.3M articles from Wikipedia in a single pass. We demonstrate that online LDA finds topic models as good or better than those found with batch VB, and in a fraction of the time.

We consider problems for which one has incomplete binary matrices that evolve with time (e.g., the votes of legislators on particular legislation, with each year characterized by a different such matrix). An objective of such analysis is to infer structure and inter-relationships underlying the matrices, here defined by latent features associated with each axis of the matrix. In addition, it is assumed that documents are available for the entities associated with at least one of the matrix axes. By jointly analyzing the matrices and documents, one may be used to inform the other within the analysis, and the model offers the opportunity to predict matrix values (e.g., votes) based only on an associated document (e.g., legislation). The research presented here merges two areas of machine-learning that have previously been investigated separately: incomplete-matrix analysis and topic modeling. The analysis is performed from a Bayesian perspective, with efficient inference constituted via Gibbs sampling. The framework is demonstrated by considering all voting data and available documents (legislation) during the 220-year lifetime of the United States Senate and House of Representatives.

This paper outlines a hierarchical Bayesian model for human category learning that learns both the organization of objects into categories, and the context in which this knowledge should be applied. The model is fit to multiple data sets, and provides a parsimonious method for describing how humans learn context specific conceptual representations.

Lifted inference algorithms for representations that combine first-order logic and probabilistic graphical models have been the focus of much recent research. All lifted algorithms developed to date are based on the same underlying idea: take a standard probabilistic inference algorithm (e.g., variable elimination, belief propagation etc.) and improve its efficiency by exploiting repeated structure in the first-order model. In this paper, we propose an approach from the other side in that we use techniques from logic for probabilistic inference. In particular, we define a set of rules that look only at the logical representation to identify models for which exact efficient inference is possible. We show that our rules yield several new tractable classes that cannot be solved efficiently by any of the existing techniques.

We propose a class of sparse coding models that utilizes a Laplacian Scale Mixture (LSM) prior to model dependencies among coefficients. Each coefficient is modeled as a Laplacian distribution with a variable scale parameter, with a Gamma distribution prior over the scale parameter. We show that, due to the conjugacy of the Gamma prior, it is possible to derive efficient inference procedures for both the coefficients and the scale parameter. When the scale parameters of a group of coefficients are combined into a single variable, it is possible to describe the dependencies that occur due to common amplitude fluctuations among coefficients, which have been shown to constitute a large fraction of the redundancy in natural images. We show that, as a consequence of this group sparse coding, the resulting inference of the coefficients follows a divisive normalization rule, and that this may be efficiently implemented a network architecture similar to that which has been proposed to occur in primary visual cortex. We also demonstrate improvements in image coding and compressive sensing recovery using the LSM model.

Upstream supervised topic models have been widely used for complicated scene understanding. However, existing maximum likelihood estimation (MLE) schemes can make the prediction model learning independent of latent topic discovery and result in an imbalanced prediction rule for scene classification. This paper presents a joint max-margin and max-likelihood learning method for upstream scene understanding models, in which latent topic discovery and prediction model estimation are closely coupled and well-balanced. The optimization problem is efficiently solved with a variational EM procedure, which iteratively solves an online loss-augmented SVM. We demonstrate the advantages of the large-margin approach on both an 8-category sports dataset and the 67-class MIT indoor scene dataset for scene categorization.

Algorithms based on iterative local approximations present a practical approach to optimal control in robotic systems. However, they generally require the temporal parameters (for e.g. the movement duration or the time point of reaching an intermediate goal) to be specified \textit{a priori}. Here, we present a methodology that is capable of jointly optimising the temporal parameters in addition to the control command profiles. The presented approach is based on a Bayesian canonical time formulation of the optimal control problem, with the temporal mapping from canonical to real time parametrised by an additional control variable. An approximate EM algorithm is derived that efficiently optimises both the movement duration and control commands offering, for the first time, a practical approach to tackling generic via point problems in a systematic way under the optimal control framework. The proposed approach is evaluated on simulations of a redundant robotic plant.